3NGD	Transferase Dna	date	Jun 11, 2010
title	Structural Basis For Proficient Incorporation Of Dttp Opposi Methylguanine By Human Dna Polymerase Iota
authors	M.G.Pence
compound		source
Molecule: 5'-D(Tpcptp(6og) Pgpgpgptpcpcptpapgpgpapcpcp(Doc))-3'; Chain: C, D Engineered: Yes		Synthetic: Yes
Molecule: Dna Polymerase Iota Chain: A Fragment: Catalytic Fragment, 1-420 Synonym: Rad30 Homolog B, Eta2 Ec: 2.7.7.7 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Poli, Rad30b Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21 Gold (De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pbg-Poli(Bi)
symmetry	Space Group: P 65 2 2	R_factor 0.215 R_Free 0.284
crystal cell	length a length b length c angle alpha angle beta angle gamma 97.999 97.999 202.552 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.80 Å
ligand	6OG, DCP, DOC	enzyme	Transferase E.C.2.7.7.7 BRENDA
Gene Ontology	Chain Function Process Component A
Primary reference	Structural basis for proficient incorporation of dTTP opposite O6-methylguanine by human DNA polymerase iota., Pence MG, Choi JY, Egli M, Guengerich FP, J Biol Chem. 2010 Dec 24;285(52):40666-72. Epub 2010 Oct 20. PMID:20961860

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk] Biological Unit Coordinates (3ngd.pdb1.gz) 134 Kb LPC: Ligand-Protein Contacts for 3NGD CSU: Contacts of Structural Units for 3NGD Structure Factors (226 Kb) Retrieve 3NGD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NGD from S2C, [Save to disk] Re-refined 3ngd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NGD in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 3NGD

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3NGD, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3ngd_A] [3ngd_D] [3ngd] [3ngd_C] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 3NGD

Community annotation for 3NGD at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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